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Compute nucleotide source annotations for CDR3 sequences

Source: R/plot_logo.R
compute_nucseq_src.Rd

For each TCR, calls .analyze_junction() to determine the V/N/D/J origin of each nucleotide in the CDR3 region. The result can be passed to plot_cdr3_logo via its nucseq_src parameter to display junction bars showing the rearrangement structure.

Usage

compute_nucseq_src(tcrs, organism, chain = c("alpha", "beta"))

Arguments

tcrs

Data.frame with columns va, ja, cdr3a, cdr3a_nucseq (for alpha chain) or vb, jb, cdr3b, cdr3b_nucseq (for beta chain).

organism

Character string. Organism identifier (e.g., "human", "mouse").

chain

Character string. "alpha" or "beta".

Value

A list of character vectors (one per TCR). Each vector has length nchar(cdr3_nucseq) with elements from c("V", "N", "J") for alpha chain, or c("V", "N1", "D", "N2", "J") for beta chain. Returns NULL for TCRs where junction analysis fails.

See also

plot_cdr3_logo, plot_junction_bars, plot_tcr_logo_panel

Examples

if (FALSE) { # \dontrun{
data(dash)
pa <- dash[dash$epitope == "PA", ][1:20, ]
src <- compute_nucseq_src(pa, organism = "mouse", chain = "beta")
plot_cdr3_logo(pa$cdr3b, chain = "beta", nucseq_src = src,
               show_junction_bars = TRUE)
} # }